| 1 | #!/usr/bin/env python |
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| 2 | # -*- coding: utf-8 -*- |
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| 3 | #************************************************************************ |
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| 4 | # TODO AP |
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| 5 | #AP |
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| 6 | # - Functionality Provided is not correct for this file |
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| 7 | # - localpythonpath should not be set in module load section! |
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| 8 | # - create a class Installation and divide installation in 3 subdefs for |
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| 9 | # ecgate, local and cca seperatly |
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| 10 | # - Change History ist nicht angepasst ans File! Original geben lassen |
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| 11 | #************************************************************************ |
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| 12 | """ |
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| 13 | @Author: Anne Fouilloux (University of Oslo) |
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| 14 | |
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| 15 | @Date: October 2014 |
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| 16 | |
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| 17 | @ChangeHistory: |
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| 18 | November 2015 - Leopold Haimberger (University of Vienna): |
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| 19 | - using the WebAPI also for general MARS retrievals |
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| 20 | - job submission on ecgate and cca |
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| 21 | - job templates suitable for twice daily operational dissemination |
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| 22 | - dividing retrievals of longer periods into digestable chunks |
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| 23 | - retrieve also longer term forecasts, not only analyses and |
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| 24 | short term forecast data |
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| 25 | - conversion into GRIB2 |
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| 26 | - conversion into .fp format for faster execution of FLEXPART |
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| 27 | |
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| 28 | February 2018 - Anne Philipp (University of Vienna): |
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| 29 | - applied PEP8 style guide |
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| 30 | - added documentation |
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| 31 | |
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| 32 | @License: |
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| 33 | (C) Copyright 2014 UIO. |
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| 34 | |
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| 35 | This software is licensed under the terms of the Apache Licence Version 2.0 |
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| 36 | which can be obtained at http://www.apache.org/licenses/LICENSE-2.0. |
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| 37 | |
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| 38 | @Requirements: |
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| 39 | - A standard python 2.6 or 2.7 installation |
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| 40 | - dateutils |
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| 41 | - matplotlib (optional, for debugging) |
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| 42 | - ECMWF specific packages, all available from https://software.ecmwf.int/ |
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| 43 | ECMWF WebMARS, gribAPI with python enabled, emoslib and |
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| 44 | ecaccess web toolkit |
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| 45 | |
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| 46 | @Description: |
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| 47 | Further documentation may be obtained from www.flexpart.eu. |
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| 48 | |
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| 49 | Functionality provided: |
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| 50 | Prepare input 3D-wind fields in hybrid coordinates + |
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| 51 | surface fields for FLEXPART runs |
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| 52 | """ |
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| 53 | # ------------------------------------------------------------------------------ |
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| 54 | # MODULES |
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| 55 | # ------------------------------------------------------------------------------ |
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| 56 | import calendar |
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| 57 | import shutil |
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| 58 | import datetime |
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| 59 | import time |
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| 60 | import os,sys,glob |
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| 61 | import subprocess |
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| 62 | import inspect |
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| 63 | # add path to submit.py to pythonpath so that python finds its buddies |
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| 64 | localpythonpath=os.path.dirname(os.path.abspath(inspect.getfile(inspect.currentframe()))) |
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| 65 | sys.path.append(localpythonpath) |
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| 66 | from UIOFiles import UIOFiles |
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| 67 | from string import strip |
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| 68 | from argparse import ArgumentParser,ArgumentDefaultsHelpFormatter |
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| 69 | from GribTools import GribTools |
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| 70 | from Control import Control |
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| 71 | from getMARSdata import getMARSdata |
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| 72 | from prepareFLEXPART import prepareFLEXPART |
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| 73 | from ECFlexpart import ECFlexpart |
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| 74 | |
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| 75 | # ------------------------------------------------------------------------------ |
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| 76 | # FUNCTIONS |
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| 77 | # ------------------------------------------------------------------------------ |
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| 78 | def install_args_and_control(): |
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| 79 | ''' |
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| 80 | @Description: |
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| 81 | Assigns the command line arguments for installation and reads |
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| 82 | control file content. Apply default values for non mentioned arguments. |
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| 83 | |
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| 84 | @Input: |
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| 85 | <nothing> |
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| 86 | |
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| 87 | @Return: |
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| 88 | args: instance of ArgumentParser |
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| 89 | Contains the commandline arguments from script/program call. |
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| 90 | |
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| 91 | c: instance of class Control |
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| 92 | Contains all necessary information of a control file. The parameters |
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| 93 | are: DAY1, DAY2, DTIME, MAXSTEP, TYPE, TIME, STEP, CLASS, STREAM, |
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| 94 | NUMBER, EXPVER, GRID, LEFT, LOWER, UPPER, RIGHT, LEVEL, LEVELIST, |
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| 95 | RESOL, GAUSS, ACCURACY, OMEGA, OMEGADIFF, ETA, ETADIFF, DPDETA, |
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| 96 | SMOOTH, FORMAT, ADDPAR, WRF, CWC, PREFIX, ECSTORAGE, ECTRANS, |
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| 97 | ECFSDIR, MAILOPS, MAILFAIL, GRIB2FLEXPART, FLEXPARTDIR |
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| 98 | For more information about format and content of the parameter see |
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| 99 | documentation. |
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| 100 | ''' |
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| 101 | parser = ArgumentParser(description='Install ECMWFDATA software locally or \ |
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| 102 | on ECMWF machines', |
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| 103 | formatter_class=ArgumentDefaultsHelpFormatter) |
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| 104 | |
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| 105 | parser.add_argument('--target', dest='install_target', |
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| 106 | help="Valid targets: local | ecgate | cca , \ |
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| 107 | the latter two are at ECMWF") |
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| 108 | parser.add_argument("--makefile", dest="makefile", |
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| 109 | help='Name of Makefile to use for compiling CONVERT2') |
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| 110 | parser.add_argument("--ecuid", dest="ecuid", |
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| 111 | help='user id at ECMWF') |
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| 112 | parser.add_argument("--ecgid", dest="ecgid", |
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| 113 | help='group id at ECMWF') |
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| 114 | parser.add_argument("--gateway", dest="gateway", |
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| 115 | help='name of local gateway server') |
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| 116 | parser.add_argument("--destination", dest="destination", |
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| 117 | help='ecaccess destination, e.g. leo@genericSftp') |
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| 118 | |
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| 119 | parser.add_argument("--flexpart_root_scripts", dest="flexpart_root_scripts", |
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| 120 | help="FLEXPART root directory on ECMWF servers \ |
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| 121 | (to find grib2flexpart and COMMAND file)\n\ |
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| 122 | Normally ECMWFDATA resides in the scripts directory \ |
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| 123 | of the FLEXPART distribution, thus the:") |
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| 124 | |
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| 125 | # arguments for job submission to ECMWF, only needed by submit.py |
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| 126 | parser.add_argument("--job_template", dest='job_template', |
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| 127 | default="job.temp.o", |
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| 128 | help="job template file for submission to ECMWF") |
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| 129 | |
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| 130 | parser.add_argument("--controlfile", dest="controlfile", |
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| 131 | default='CONTROL.temp', |
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| 132 | help="file with control parameters") |
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| 133 | |
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| 134 | args = parser.parse_args() |
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| 135 | |
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| 136 | try: |
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| 137 | c = Control(args.controlfile) |
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| 138 | except: |
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| 139 | print('Could not read control file "' + args.controlfile + '"') |
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| 140 | print('Either it does not exist or its syntax is wrong.') |
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| 141 | print('Try "' + sys.argv[0].split('/')[-1] + |
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| 142 | ' -h" to print usage information') |
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| 143 | exit(1) |
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| 144 | |
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| 145 | if args.install_target != 'local': |
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| 146 | if (args.ecgid is None or args.ecuid is None or args.gateway is None |
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| 147 | or args.destination is None): |
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| 148 | print('Please enter your ECMWF user id and group id as well as \ |
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| 149 | the \nname of the local gateway and the ectrans \ |
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| 150 | destination ') |
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| 151 | print('with command line options --ecuid --ecgid \ |
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| 152 | --gateway --destination') |
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| 153 | print('Try "' + sys.argv[0].split('/')[-1] + |
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| 154 | ' -h" to print usage information') |
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| 155 | print('Please consult ecaccess documentation or ECMWF user support \ |
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| 156 | for further details') |
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| 157 | sys.exit(1) |
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| 158 | else: |
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| 159 | c.ecuid = args.ecuid |
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| 160 | c.ecgid = args.ecgid |
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| 161 | c.gateway = args.gateway |
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| 162 | c.destination = args.destination |
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| 163 | |
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| 164 | try: |
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| 165 | c.makefile = args.makefile |
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| 166 | except: |
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| 167 | pass |
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| 168 | |
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| 169 | if args.install_target == 'local': |
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| 170 | if args.flexpart_root_scripts is None: |
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| 171 | c.flexpart_root_scripts = '../' |
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| 172 | else: |
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| 173 | c.flexpart_root_scripts = args.flexpart_root_scripts |
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| 174 | |
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| 175 | if args.install_target != 'local': |
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| 176 | if args.flexpart_root_scripts is None: |
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| 177 | c.ec_flexpart_root_scripts = '${HOME}' |
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| 178 | else: |
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| 179 | c.ec_flexpart_root_scripts = args.flexpart_root_scripts |
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| 180 | |
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| 181 | return args, c |
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| 182 | |
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| 183 | |
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| 184 | def main(): |
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| 185 | ''' |
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| 186 | ''' |
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| 187 | os.chdir(localpythonpath) |
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| 188 | args, c = install_args_and_control() |
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| 189 | if args.install_target is not None: |
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| 190 | install_via_gateway(c, args.install_target) |
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| 191 | else: |
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| 192 | print('Please specify installation target (local|ecgate|cca)') |
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| 193 | print('use -h or --help for help') |
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| 194 | sys.exit() |
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| 195 | |
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| 196 | def install_via_gateway(c, target): |
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| 197 | |
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| 198 | ecd = c.ecmwfdatadir |
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| 199 | template = ecd + 'python/compilejob.temp' |
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| 200 | job = ecd + 'python/compilejob.ksh' |
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| 201 | fo = open(job, 'w') |
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| 202 | #AP could do with open(template) as f, open(job, 'w') as fo: |
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| 203 | #AP or nested with statements |
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| 204 | with open(template) as f: |
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| 205 | fdata = f.read().split('\n') |
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| 206 | for data in fdata: |
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| 207 | if 'MAKEFILE=' in data: |
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| 208 | if c.makefile is not None: |
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| 209 | data = 'export MAKEFILE=' + c.makefile |
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| 210 | if 'FLEXPART_ROOT_SCRIPTS=' in data: |
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| 211 | if c.flexpart_root_scripts != '../': |
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| 212 | data = 'export FLEXPART_ROOT_SCRIPTS=' + \ |
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| 213 | c.flexpart_root_scripts |
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| 214 | else: |
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| 215 | data='export FLEXPART_ROOT_SCRIPTS=$HOME' |
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| 216 | if target.lower() != 'local': |
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| 217 | if '--workdir' in data: |
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| 218 | data = '#SBATCH --workdir=/scratch/ms/' + c.ecgid + \ |
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| 219 | '/' + c.ecuid |
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| 220 | if '##PBS -o' in data: |
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| 221 | data = '##PBS -o /scratch/ms/' + c.ecgid + '/' + c.ecuid + \ |
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| 222 | 'flex_ecmwf.$Jobname.$Job_ID.out' |
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| 223 | if 'FLEXPART_ROOT_SCRIPTS=' in data: |
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| 224 | if c.ec_flexpart_root_scripts != '../': |
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| 225 | data = 'export FLEXPART_ROOT_SCRIPTS=' + \ |
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| 226 | c.ec_flexpart_root_scripts |
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| 227 | else: |
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| 228 | data = 'export FLEXPART_ROOT_SCRIPTS=$HOME' |
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| 229 | fo.write(data + '\n') |
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| 230 | f.close() |
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| 231 | fo.close() |
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| 232 | |
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| 233 | if target.lower() != 'local': |
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| 234 | template = ecd + 'python/job.temp.o' |
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| 235 | #AP hier eventuell Zeile für Zeile lesen und dann if Entscheidung |
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| 236 | with open(template) as f: |
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| 237 | fdata = f.read().split('\n') |
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| 238 | f.close() |
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| 239 | fo = open(template[:-2], 'w') |
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| 240 | for data in fdata: |
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| 241 | if '--workdir' in data: |
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| 242 | data = '#SBATCH --workdir=/scratch/ms/' + c.ecgid + \ |
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| 243 | '/' + c.ecuid |
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| 244 | if '##PBS -o' in data: |
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| 245 | data = '##PBS -o /scratch/ms/' + c.ecgid + '/' + \ |
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| 246 | c.ecuid + 'flex_ecmwf.$Jobname.$Job_ID.out' |
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| 247 | if 'export PATH=${PATH}:' in data: |
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| 248 | data += c.ec_flexpart_root_scripts + '/ECMWFDATA7.1/python' |
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| 249 | if 'cat>>' in data or 'cat >>' in data: |
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| 250 | i = data.index('>') |
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| 251 | fo.write(data[:i] + data[i+1:] + '\n') |
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| 252 | fo.write('GATEWAY ' + c.gateway + '\n') |
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| 253 | fo.write('DESTINATION ' + c.destination + '\n') |
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| 254 | fo.write('EOF\n') |
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| 255 | |
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| 256 | fo.write(data + '\n') |
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| 257 | fo.close() |
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| 258 | |
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| 259 | job = ecd + 'python/ECMWF_ENV' |
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| 260 | with open(job, 'w') as fo: |
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| 261 | fo.write('ECUID ' + c.ecuid + '\n') |
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| 262 | fo.write('ECGID ' + c.ecgid + '\n') |
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| 263 | fo.write('GATEWAY ' + c.gateway + '\n') |
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| 264 | fo.write('DESTINATION ' + c.destination + '\n') |
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| 265 | fo.close() |
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| 266 | |
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| 267 | |
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| 268 | |
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| 269 | if target.lower() == 'local': |
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| 270 | # compile CONVERT2 |
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| 271 | if c.flexpart_root_scripts is None or c.flexpart_root_scripts == '../': |
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| 272 | print('Warning: FLEXPART_ROOT_SCRIPTS has not been specified') |
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| 273 | print('Only CONVERT2 will be compiled in ' + ecd + '/../src') |
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| 274 | else: |
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| 275 | c.flexpart_root_scripts = os.path.expandvars(os.path.expanduser( |
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| 276 | c.flexpart_root_scripts)) |
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| 277 | if os.path.abspath(ecd) != os.path.abspath(c.flexpart_root_scripts): |
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| 278 | os.chdir('/') |
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| 279 | p = subprocess.check_call(['tar', '-cvf', |
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| 280 | ecd + '../ECMWFDATA7.1.tar', |
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| 281 | ecd + 'python', |
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| 282 | ecd + 'grib_templates', |
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| 283 | ecd + 'src']) |
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| 284 | try: |
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| 285 | os.makedirs(c.flexpart_root_scripts + '/ECMWFDATA7.1') |
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| 286 | except: |
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| 287 | pass |
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| 288 | os.chdir(c.flexpart_root_scripts + '/ECMWFDATA7.1') |
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| 289 | p = subprocess.check_call(['tar', '-xvf', |
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| 290 | ecd + '../ECMWFDATA7.1.tar']) |
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| 291 | os.chdir(c.flexpart_root_scripts + '/ECMWFDATA7.1/src') |
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| 292 | |
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| 293 | os.chdir('../src') |
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| 294 | print(('install ECMWFDATA7.1 software on ' + target + ' in directory ' |
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| 295 | + os.getcwd())) |
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| 296 | if c.makefile is None: |
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| 297 | makefile = 'Makefile.local.ifort' |
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| 298 | else: |
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| 299 | makefile = c.makefile |
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| 300 | flist = glob.glob('*.mod') + glob.glob('*.o') |
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| 301 | if flist: |
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| 302 | p = subprocess.check_call(['rm'] + flist) |
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| 303 | try: |
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| 304 | print(('Using makefile: ' + makefile)) |
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| 305 | p = subprocess.check_call(['make', '-f', makefile]) |
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| 306 | p = subprocess.check_call(['ls', '-l','CONVERT2']) |
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| 307 | except: |
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| 308 | print('compile failed - please edit ' + makefile + |
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| 309 | ' or try another Makefile in the src directory.') |
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| 310 | print('most likely GRIB_API_INCLUDE_DIR, GRIB_API_LIB ' |
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| 311 | 'and EMOSLIB must be adapted.') |
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| 312 | print('Available Makefiles:') |
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| 313 | print(glob.glob('Makefile*')) |
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| 314 | |
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| 315 | elif target.lower() == 'ecgate': |
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| 316 | os.chdir('/') |
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| 317 | p = subprocess.check_call(['tar', '-cvf', |
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| 318 | ecd + '../ECMWFDATA7.1.tar', |
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| 319 | ecd + 'python', |
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| 320 | ecd + 'grib_templates', |
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| 321 | ecd + 'src']) |
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| 322 | try: |
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| 323 | p = subprocess.check_call(['ecaccess-file-put', |
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| 324 | ecd + '../ECMWFDATA7.1.tar', |
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| 325 | 'ecgate:/home/ms/' + c.ecgid + '/' + |
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| 326 | c.ecuid + '/ECMWFDATA7.1.tar']) |
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| 327 | except: |
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| 328 | print('ecaccess-file-put failed! Probably the eccert key has expired.') |
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| 329 | exit(1) |
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| 330 | p = subprocess.check_call(['ecaccess-job-submit', |
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| 331 | '-queueName', |
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| 332 | target, |
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| 333 | ecd + 'python/compilejob.ksh']) |
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| 334 | print('compilejob.ksh has been submitted to ecgate for ' |
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| 335 | 'installation in ' + c.ec_flexpart_root_scripts + |
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| 336 | '/ECMWFDATA7.1') |
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| 337 | print('You should get an email with subject flexcompile within ' |
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| 338 | 'the next few minutes') |
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| 339 | |
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| 340 | elif target.lower() == 'cca': |
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| 341 | os.chdir('/') |
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| 342 | p = subprocess.check_call(['tar', '-cvf', |
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| 343 | ecd + '../ECMWFDATA7.1.tar', |
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| 344 | ecd + 'python', |
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| 345 | ecd + 'grib_templates', |
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| 346 | ecd + 'src']) |
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| 347 | try: |
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| 348 | p = subprocess.check_call(['ecaccess-file-put', |
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| 349 | ecd + '../ECMWFDATA7.1.tar', |
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| 350 | 'cca:/home/ms/' + c.ecgid + '/' + |
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| 351 | c.ecuid + '/ECMWFDATA7.1.tar']) |
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| 352 | except: |
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| 353 | print('ecaccess-file-put failed! ' |
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| 354 | 'Probably the eccert key has expired.') |
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| 355 | exit(1) |
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| 356 | |
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| 357 | p=subprocess.check_call(['ecaccess-job-submit', |
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| 358 | '-queueName', |
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| 359 | target, |
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| 360 | ecd + 'python/compilejob.ksh']) |
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| 361 | print('compilejob.ksh has been submitted to cca for installation in ' + |
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| 362 | c.ec_flexpart_root_scripts + '/ECMWFDATA7.1') |
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| 363 | print('You should get an email with subject flexcompile ' |
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| 364 | 'within the next few minutes') |
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| 365 | |
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| 366 | else: |
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| 367 | print('ERROR: unknown installation target ', target) |
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| 368 | print('Valid targets: ecgate, cca, local') |
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| 369 | |
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| 370 | return |
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| 371 | |
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| 372 | |
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| 373 | if __name__ == "__main__": |
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| 374 | main() |
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